Published March 4, 2024 | Version v1
Dataset Open

Data from: The spotted parrotfish genome provides evolutionary insight into the ecological adaptation of a keystone dietary specialist

  • 1. Australian Museum Research Institute*
  • 2. Fudan University
  • 3. University of Sydney
  • 4. Pennsylvania State University
  • 5. Griffith University

Description

With over 600 valid species, the wrasses (family Labridae) are among the largest and most successful of the marine teleosts. They feature prominently on coral reefs where they are known not only for their impressive diversity in colouration and form, but also in their functional specialization and ability to occupy a wide variety of trophic guilds. Among the wrasses, the parrotfishes (tribe Scarini) display some one of the most dramatic examples of trophic specialization. Using abrasion-resistant biomineralized teeth, parrotfishes are able to mechanically extract protein-rich micro-photoautotrophs growing in and amongst reef carbonate material, a dietary niche that is inaccessible to most other teleost fishes. This ability to exploit an otherwise untapped trophic resource is thought to have played a role in the diversification and evolutionary success of the parrotfishes. In order to better understand the key evolutionary innovations leading to the success of these dietary specialists, we sequenced and analysed the genome of a representative species, the spotted parrotfish (Cetoscarus ocellatus). We find significant expansion, selection, and duplication within several detoxification gene families and a novel poly-glutamine expansion in the enamel protein ameloblastin, and we consider their evolutionary implications. Our genome provides a useful resource for comparative genomic studies investigating the evolutionary history of this highly specialized teleostean radiation.

Notes

Funding provided by: University of Sydney
Crossref Funder Registry ID: https://ror.org/0384j8v12
Award Number:

Funding provided by: National Key R&D Program of China
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100012166
Award Number: 2020YFE0201600

Funding provided by: National Key R&D Program of China
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100012166
Award Number: 2021YFC2500202

Funding provided by: National Natural Science Foundation of China
Crossref Funder Registry ID: https://ror.org/01h0zpd94
Award Number: 31970563

Funding provided by: 111 Project
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100013314
Award Number: B13016

Funding provided by: Science and Technology Commission of Shanghai Municipality
Crossref Funder Registry ID: https://ror.org/03kt66j61
Award Number: 2017SHZDZX01

Funding provided by: Science and Technology Commission of Shanghai Municipality
Crossref Funder Registry ID: https://ror.org/03kt66j61
Award Number: 19410741100

Methods

The spotted parrotfish genomes (Cetoscarus ocellatus) was sequenced and assembled to investigate the evolution of this coral reef fish group, and to provide genomic resources for studies on the Scarini. This genome was assembled using a combination of long-read, linked-read, and Hi-C data (the raw seqeunce data are avalable on the SRA database under BioProject accession PRJNA1081164). Assembly methods are outlined in the associated manuscript. Briefly, an initial de novo assembly of the PacBio long-read data was performed using Canu v.2.1.1 with default settings and an estimated genome size of 1.4 Gb (based on published labrid genomes). TELL-seq linked reads were used to scaffold the draft de novo long-read assembly and improve its contiguity using Long Ranger basic v2.2.2, ARCS v1.2, and LINKS v1.8.7. Finally, Hi-C reads were aligned to the ARCS/LINKS-scaffolded draft assembly. The genome was annotated using FGENESH++.

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